Incidental Mutation 'R6846:Nlgn1'
ID 534752
Institutional Source Beutler Lab
Gene Symbol Nlgn1
Ensembl Gene ENSMUSG00000063887
Gene Name neuroligin 1
Synonyms NL1, Nlg1, 6330415N05Rik
MMRRC Submission 044952-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R6846 (G1)
Quality Score 225.009
Status Validated
Chromosome 3
Chromosomal Location 25480379-26386609 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 25490506 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 378 (V378A)
Ref Sequence ENSEMBL: ENSMUSP00000142086 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000075054] [ENSMUST00000108308] [ENSMUST00000191835] [ENSMUST00000193603]
AlphaFold Q99K10
Predicted Effect probably damaging
Transcript: ENSMUST00000075054
AA Change: V407A

PolyPhen 2 Score 0.978 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000074565
Gene: ENSMUSG00000063887
AA Change: V407A

DomainStartEndE-ValueType
Pfam:COesterase 29 626 4.8e-199 PFAM
Pfam:Abhydrolase_3 196 302 2.2e-8 PFAM
transmembrane domain 697 719 N/A INTRINSIC
low complexity region 720 731 N/A INTRINSIC
low complexity region 796 809 N/A INTRINSIC
low complexity region 816 827 N/A INTRINSIC
low complexity region 829 839 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000108308
AA Change: V378A

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000103944
Gene: ENSMUSG00000063887
AA Change: V378A

DomainStartEndE-ValueType
Pfam:COesterase 29 597 2.5e-190 PFAM
Pfam:Abhydrolase_3 176 306 4.3e-8 PFAM
transmembrane domain 668 690 N/A INTRINSIC
low complexity region 691 702 N/A INTRINSIC
low complexity region 767 780 N/A INTRINSIC
low complexity region 787 798 N/A INTRINSIC
low complexity region 800 810 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000191835
AA Change: V378A

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000142086
Gene: ENSMUSG00000063887
AA Change: V378A

DomainStartEndE-ValueType
Pfam:COesterase 29 597 2.5e-190 PFAM
Pfam:Abhydrolase_3 176 306 4.3e-8 PFAM
transmembrane domain 668 690 N/A INTRINSIC
low complexity region 691 702 N/A INTRINSIC
low complexity region 767 780 N/A INTRINSIC
low complexity region 787 798 N/A INTRINSIC
low complexity region 800 810 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000193603
AA Change: V407A

PolyPhen 2 Score 0.978 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000142200
Gene: ENSMUSG00000063887
AA Change: V407A

DomainStartEndE-ValueType
Pfam:COesterase 29 626 1.2e-186 PFAM
Pfam:Abhydrolase_3 196 309 3.7e-8 PFAM
transmembrane domain 697 719 N/A INTRINSIC
low complexity region 720 731 N/A INTRINSIC
low complexity region 796 809 N/A INTRINSIC
low complexity region 816 827 N/A INTRINSIC
low complexity region 829 839 N/A INTRINSIC
Meta Mutation Damage Score 0.1304 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.4%
  • 20x: 97.9%
Validation Efficiency 100% (42/42)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of a family of neuronal cell surface proteins. Members of this family may act as splice site-specific ligands for beta-neurexins and may be involved in the formation and remodeling of central nervous system synapses. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a knock-out allele are viable and fertile but display impaired NMDA receptor-mediated synaptic transmission onto CA1 pyramidal cells. [provided by MGI curators]
Allele List at MGI

All alleles(4) : Targeted(3) Gene trapped(1)

Other mutations in this stock
Total: 42 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Ahnak A G 19: 8,989,221 (GRCm39) N3502D possibly damaging Het
Ambn T A 5: 88,609,574 (GRCm39) I94K possibly damaging Het
Ank3 A G 10: 69,660,179 (GRCm39) H227R probably damaging Het
Arhgap42 G T 9: 9,006,446 (GRCm39) P650Q probably damaging Het
Bahcc1 A G 11: 120,162,422 (GRCm39) E240G possibly damaging Het
Cd19 T C 7: 126,010,025 (GRCm39) E408G probably benign Het
Cdh11 G A 8: 103,391,276 (GRCm39) T320I probably damaging Het
Cep131 G A 11: 119,956,517 (GRCm39) R944W probably damaging Het
Dgkd T G 1: 87,853,413 (GRCm39) probably null Het
Dnaaf1 T A 8: 120,309,401 (GRCm39) L163Q probably damaging Het
Ecpas A G 4: 58,814,081 (GRCm39) C1342R possibly damaging Het
Etl4 T A 2: 20,748,919 (GRCm39) L550Q possibly damaging Het
Evpl T C 11: 116,114,633 (GRCm39) E1019G probably damaging Het
Fam120b T C 17: 15,635,091 (GRCm39) L601P probably damaging Het
Fhit C A 14: 9,763,762 (GRCm38) R172L possibly damaging Het
Hoxa6 T C 6: 52,183,523 (GRCm39) H174R possibly damaging Het
Htra4 A G 8: 25,520,561 (GRCm39) F367L probably damaging Het
Ighg2c A G 12: 113,251,930 (GRCm39) I102T unknown Het
Iws1 T C 18: 32,219,326 (GRCm39) probably benign Het
Lats2 A G 14: 57,933,591 (GRCm39) V842A probably damaging Het
Limd2 C T 11: 106,050,213 (GRCm39) M1I probably null Het
Lrp2 T A 2: 69,348,787 (GRCm39) Q728L probably damaging Het
Mcc T A 18: 44,606,707 (GRCm39) T400S possibly damaging Het
Mthfd1l A G 10: 3,997,898 (GRCm39) D623G probably damaging Het
Myocos T C 1: 162,484,665 (GRCm39) probably benign Het
Nat1 G T 8: 67,943,995 (GRCm39) A124S probably benign Het
Nfya A T 17: 48,702,715 (GRCm39) M62K probably benign Het
Or52r1c T A 7: 102,735,265 (GRCm39) I175N possibly damaging Het
Or5ak22 A T 2: 85,230,861 (GRCm39) N5K probably damaging Het
Pitpnm2 T C 5: 124,269,234 (GRCm39) S463G probably benign Het
Serpinb3b T C 1: 107,082,403 (GRCm39) E287G probably benign Het
Slc16a13 T C 11: 70,108,661 (GRCm39) T390A probably benign Het
Slc7a14 A G 3: 31,278,372 (GRCm39) M411T probably damaging Het
Strn A G 17: 79,043,886 (GRCm39) F11L probably damaging Het
Swap70 T A 7: 109,854,956 (GRCm39) F85L possibly damaging Het
Tanc2 T A 11: 105,689,479 (GRCm39) W214R probably benign Het
Tenm3 T C 8: 48,729,773 (GRCm39) K1411R probably benign Het
Tmem176a G T 6: 48,820,759 (GRCm39) R116L probably damaging Het
Trim71 G T 9: 114,354,115 (GRCm39) H296Q probably damaging Het
Vmn1r67 A T 7: 10,180,840 (GRCm39) I35L probably benign Het
Vnn3 A G 10: 23,727,620 (GRCm39) T47A probably benign Het
Zscan10 A T 17: 23,824,581 (GRCm39) Q12H probably damaging Het
Other mutations in Nlgn1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00510:Nlgn1 APN 3 25,490,654 (GRCm39) missense probably benign 0.02
IGL00543:Nlgn1 APN 3 25,487,945 (GRCm39) missense probably damaging 1.00
IGL00960:Nlgn1 APN 3 25,966,861 (GRCm39) missense probably damaging 1.00
IGL01533:Nlgn1 APN 3 25,490,527 (GRCm39) missense possibly damaging 0.69
IGL02146:Nlgn1 APN 3 25,966,846 (GRCm39) missense probably damaging 0.96
IGL02616:Nlgn1 APN 3 25,488,409 (GRCm39) missense probably damaging 0.99
IGL03342:Nlgn1 APN 3 26,187,411 (GRCm39) missense probably damaging 1.00
ligation UTSW 3 25,490,199 (GRCm39) nonsense probably null
G1citation:Nlgn1 UTSW 3 26,187,796 (GRCm39) missense probably benign 0.00
P0018:Nlgn1 UTSW 3 25,490,741 (GRCm39) missense probably damaging 1.00
R0010:Nlgn1 UTSW 3 25,490,006 (GRCm39) splice site probably benign
R0010:Nlgn1 UTSW 3 25,490,006 (GRCm39) splice site probably benign
R0123:Nlgn1 UTSW 3 25,490,089 (GRCm39) missense probably damaging 1.00
R0134:Nlgn1 UTSW 3 25,490,089 (GRCm39) missense probably damaging 1.00
R0294:Nlgn1 UTSW 3 26,187,625 (GRCm39) missense probably benign 0.23
R0798:Nlgn1 UTSW 3 25,488,410 (GRCm39) missense probably benign 0.05
R1051:Nlgn1 UTSW 3 25,966,869 (GRCm39) missense probably damaging 0.98
R1116:Nlgn1 UTSW 3 25,488,038 (GRCm39) missense probably benign 0.00
R1289:Nlgn1 UTSW 3 25,488,400 (GRCm39) missense possibly damaging 0.87
R1522:Nlgn1 UTSW 3 25,490,073 (GRCm39) missense probably damaging 1.00
R1550:Nlgn1 UTSW 3 25,966,808 (GRCm39) missense probably damaging 1.00
R1669:Nlgn1 UTSW 3 25,490,298 (GRCm39) missense probably damaging 1.00
R1853:Nlgn1 UTSW 3 26,187,671 (GRCm39) missense possibly damaging 0.80
R1856:Nlgn1 UTSW 3 25,494,201 (GRCm39) nonsense probably null
R1935:Nlgn1 UTSW 3 26,385,939 (GRCm39) utr 5 prime probably benign
R1936:Nlgn1 UTSW 3 26,385,939 (GRCm39) utr 5 prime probably benign
R1952:Nlgn1 UTSW 3 25,490,464 (GRCm39) missense probably damaging 1.00
R1953:Nlgn1 UTSW 3 25,490,464 (GRCm39) missense probably damaging 1.00
R2004:Nlgn1 UTSW 3 25,488,034 (GRCm39) missense probably benign 0.29
R2114:Nlgn1 UTSW 3 26,187,414 (GRCm39) missense probably damaging 1.00
R2116:Nlgn1 UTSW 3 26,187,414 (GRCm39) missense probably damaging 1.00
R2198:Nlgn1 UTSW 3 25,487,925 (GRCm39) missense probably damaging 0.99
R2994:Nlgn1 UTSW 3 25,490,162 (GRCm39) missense probably damaging 1.00
R3056:Nlgn1 UTSW 3 25,487,860 (GRCm39) missense possibly damaging 0.53
R4190:Nlgn1 UTSW 3 25,488,062 (GRCm39) missense probably benign
R4196:Nlgn1 UTSW 3 25,488,556 (GRCm39) missense probably damaging 1.00
R4613:Nlgn1 UTSW 3 25,490,186 (GRCm39) missense probably benign 0.01
R4654:Nlgn1 UTSW 3 26,187,850 (GRCm39) missense possibly damaging 0.51
R4757:Nlgn1 UTSW 3 25,490,507 (GRCm39) missense possibly damaging 0.63
R4757:Nlgn1 UTSW 3 25,490,332 (GRCm39) missense probably damaging 1.00
R4815:Nlgn1 UTSW 3 25,490,194 (GRCm39) missense probably damaging 0.99
R4884:Nlgn1 UTSW 3 25,966,838 (GRCm39) missense probably damaging 1.00
R4966:Nlgn1 UTSW 3 25,974,401 (GRCm39) missense possibly damaging 0.65
R5119:Nlgn1 UTSW 3 25,487,958 (GRCm39) missense probably damaging 0.99
R5842:Nlgn1 UTSW 3 26,187,892 (GRCm39) splice site probably null
R6218:Nlgn1 UTSW 3 25,490,257 (GRCm39) missense probably damaging 1.00
R6397:Nlgn1 UTSW 3 25,487,827 (GRCm39) missense possibly damaging 0.53
R6500:Nlgn1 UTSW 3 25,488,094 (GRCm39) missense possibly damaging 0.84
R6822:Nlgn1 UTSW 3 26,187,796 (GRCm39) missense probably benign 0.00
R7047:Nlgn1 UTSW 3 25,490,199 (GRCm39) nonsense probably null
R7147:Nlgn1 UTSW 3 26,187,509 (GRCm39) missense probably benign 0.02
R7754:Nlgn1 UTSW 3 25,488,467 (GRCm39) missense probably damaging 1.00
R7886:Nlgn1 UTSW 3 25,490,071 (GRCm39) missense probably damaging 1.00
R8184:Nlgn1 UTSW 3 25,490,363 (GRCm39) missense probably damaging 1.00
R8261:Nlgn1 UTSW 3 25,487,816 (GRCm39) missense possibly damaging 0.53
R8304:Nlgn1 UTSW 3 26,187,534 (GRCm39) missense probably damaging 1.00
R8364:Nlgn1 UTSW 3 25,490,140 (GRCm39) missense probably benign 0.00
R8503:Nlgn1 UTSW 3 26,187,522 (GRCm39) missense probably damaging 0.99
R9035:Nlgn1 UTSW 3 25,488,595 (GRCm39) missense probably damaging 1.00
R9053:Nlgn1 UTSW 3 25,488,607 (GRCm39) missense probably damaging 1.00
R9209:Nlgn1 UTSW 3 25,966,804 (GRCm39) critical splice donor site probably null
R9268:Nlgn1 UTSW 3 25,490,548 (GRCm39) missense probably damaging 0.96
R9368:Nlgn1 UTSW 3 25,488,622 (GRCm39) missense probably damaging 0.99
R9492:Nlgn1 UTSW 3 25,488,480 (GRCm39) nonsense probably null
R9596:Nlgn1 UTSW 3 25,488,587 (GRCm39) missense probably damaging 1.00
R9647:Nlgn1 UTSW 3 25,488,182 (GRCm39) missense probably damaging 1.00
R9697:Nlgn1 UTSW 3 25,494,035 (GRCm39) missense possibly damaging 0.52
Z1176:Nlgn1 UTSW 3 25,490,768 (GRCm39) missense probably benign 0.12
Predicted Primers PCR Primer
(F):5'- ACCCATTGATGGTCCGTAAAC -3'
(R):5'- GAATGCCTGCAGAAGAAGCC -3'

Sequencing Primer
(F):5'- TTGATGGTCCGTAAACAAAGCC -3'
(R):5'- GAAGCCTTACAAAGAACTTGTTGATC -3'
Posted On 2018-09-12